Multiple platform build/check report for BioC 3.21 - BUILD results for SCArray.sat on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4777
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4545
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4576
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4528
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4458
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

BUILD results for SCArray.sat on lconway

To the developers/maintainers of the SCArray.sat package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SCArray.sat.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: SCArray.sat

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SCArray.sat

StartedAt: 2025-03-19 18:34:21 -0400 (Wed, 19 Mar 2025)

EndedAt: 2025-03-19 18:35:51 -0400 (Wed, 19 Mar 2025)

EllapsedTime: 90.2 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SCArray.sat
###
##############################################################################
##############################################################################


* checking for file ‘SCArray.sat/DESCRIPTION’ ... OK
* preparing ‘SCArray.sat’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘SCArray.sat.Rmd’ using rmarkdown

  |                                                                      
  |                                                                |   0%
  |                                                                      
  |================================================================| 100%

Quitting from SCArray.sat.Rmd:78-101 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! non-numeric argument to binary operator
---
Backtrace:
     ▆
  1. ├─Seurat::ScaleData(d)
  2. └─Seurat:::ScaleData.Seurat(d)
  3.   ├─Seurat::ScaleData(...)
  4.   └─Seurat:::ScaleData.Assay(...)
  5.     ├─SeuratObject::SetAssayData(...)
  6.     ├─SCArray.sat:::SetAssayData.SCArrayAssay(...)
  7.     │ └─SeuratObject::IsMatrixEmpty(new.data)
  8.     ├─Seurat::ScaleData(...)
  9.     └─SCArray.sat:::ScaleData.SC_GDSMatrix(...)
 10.       ├─BiocGenerics::lapply(...)
 11.       └─base::lapply(...)
 12.         └─SCArray.sat (local) FUN(X[[i]], ...)
 13.           └─SCArray.sat:::.x_row_scale(m, do.center, do.scale, scale.max)
 14.             ├─SCArray::scRowMeanVar(x, na.rm = TRUE)
 15.             └─SCArray::scRowMeanVar(x, na.rm = TRUE)
 16.               └─SCArray:::.x_row_mean_var(x, na.rm, ...)
 17.                 └─SCArray:::.parallel_col_reduce(...)
 18.                   └─DelayedArray::blockReduce(...)
 19.                     └─DelayedArray::gridReduce(...)
 20.                       └─DelayedArray (local) FUN(viewport, init, ...)
 21.                         └─S4Arrays::read_block(x, viewport, as.sparse = as.sparse)
 22.                           └─S4Arrays:::.read_block(x, viewport, as.sparse = as.sparse)
 23.                             ├─SparseArray::read_block_as_sparse(x, viewport)
 24.                             └─SparseArray::read_block_as_sparse(x, viewport)
 25.                               ├─SparseArray::extract_sparse_array(x, Nindex)
 26.                               └─DelayedArray::extract_sparse_array(x, Nindex)
 27.                                 ├─SparseArray::extract_sparse_array(x@seed, index)
 28.                                 └─DelayedArray::extract_sparse_array(x@seed, index)
 29.                                   ├─SparseArray::extract_sparse_array(x@seed, index)
 30.                                   └─DelayedArray::extract_sparse_array(x@seed, index)
 31.                                     ├─SparseArray::extract_sparse_array(x@seed, seed_index)
 32.                                     └─DelayedArray::extract_sparse_array(x@seed, seed_index)
 33.                                       ├─BiocGenerics::do.call(x@OP, c(Largs, list(svt), Rargs))
 34.                                       └─base::do.call(x@OP, c(Largs, list(svt), Rargs))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'SCArray.sat.Rmd' failed with diagnostics:
non-numeric argument to binary operator
--- failed re-building ‘SCArray.sat.Rmd’

SUMMARY: processing the following file failed:
  ‘SCArray.sat.Rmd’

Error: Vignette re-building failed.
Execution halted